Effects of differing salinities on morphological characters have been found in marine and brackish populations of Tisbe holothuriae. The results suggested an active role of salinity as a factor promoting divergence. In order to test if the observed differentiation could be due to the level of heterozygosity, a study was performed in strains with low and high homozygosity. Six quantitative traits, and their respective fluctuating asymmetry, have been measured in outbred (coefficient of consanguineity, F = 0) and inbred (F = 0.5) strains, raised at three salinities; 20, 25 and 35‰. The analysis of variance was applied to test if the morphological measures were the same, and if the variations induced by decreased salinity had the same trend, in the two strains. Wilcoxon test was applied to the asymmetry, when it was not possible to render the variances homogeneous. The results showed that the measures and the effects of salinity on morphometry differed in the strains with low and high homozygosity. No effect of salinity on asymmetry was found. Length measures showed higher asymmetry in the most homozygous strain.